4ZMH

Crystal structure of a five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Biochemical and Structural Characterization of a Five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T.

Wang, W.Yan, R.Nocek, B.P.Vuong, T.V.Di Leo, R.Xu, X.Cui, H.Gatenholm, P.Toriz, G.Tenkanen, M.Savchenko, A.Master, E.R.

(2016) J Biol Chem 291: 14120-14133

  • DOI: 10.1074/jbc.M115.702944
  • Primary Citation of Related Structures:  
    4ZMH

  • PubMed Abstract: 
  • Glucuronic acid (GlcAp) and/or methylglucuronic acid (MeGlcAp) decorate the major forms of xylan in hardwood and coniferous softwoods as well as many cereal grains. Accordingly, the complete utilization of glucuronoxylans or conversion to sugar precursors requires the action of main chain xylanases as well as α-glucuronidases that release the α- (1→2)-linked (Me)GlcAp side groups ...

    Glucuronic acid (GlcAp) and/or methylglucuronic acid (MeGlcAp) decorate the major forms of xylan in hardwood and coniferous softwoods as well as many cereal grains. Accordingly, the complete utilization of glucuronoxylans or conversion to sugar precursors requires the action of main chain xylanases as well as α-glucuronidases that release the α- (1→2)-linked (Me)GlcAp side groups. Herein, a family GH115 enzymefrom the marine bacterium Saccharophagus degradans 2-40(T), SdeAgu115A, demonstrated activity toward glucuronoxylan and oligomers thereof with preference toward MeGlcAp linked to internal xylopyranosyl residues. Unique biochemical characteristics of NaCl activation were also observed. The crystal structure of SdeAgu115A revealed a five-domain architecture, with an additional insertion C(+) domain that had significant impact on the domain arrangement of SdeAgu115A monomer and its dimerization. The participation of domain C(+) in substrate binding was supported by reduced substrate inhibition upon introducing W773A, W689A, and F696A substitutions within this domain. In addition to Asp-335, the catalytic essentiality of Glu-216 was revealed by site-specific mutagenesis. A primary sequence analysis suggested that the SdeAgu115A architecture is shared by more than half of GH115 members, thus defining a distinct archetype for GH115 enzymes.


    Organizational Affiliation

    From the Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada, emma.master@utoronto.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA, B939Saccharophagus degradans 2-40Mutation(s): 0 
Gene Names: Sde_1755
UniProt
Find proteins for Q21JW4 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024))
Explore Q21JW4 
Go to UniProtKB:  Q21JW4
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.442α = 90
b = 124.294β = 90
c = 180.027γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2016-05-18
    Changes: Structure summary
  • Version 1.3: 2016-07-13
    Changes: Database references